/**
 * @file src/Functions/isCanonicalPairing.cpp
 *
 * @section DESCRIPTION
 * Stores the enumerateNucleotide function.
 *
 * @date 23-may-2013
 *
 * @author Youri Hoogstrate
 *
 * @section LICENSE
 * yh-kt-fold can predict RNA 2D structures including K-turns.
 * Copyright (C) 2012-2013 Youri Hoogstrate
 *
 * This file is part of yh-kt-fold.
 *
 * yh-kt-fold is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * yh-kt-fold is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program. If not, see <http://www.gnu.org/licenses/>.
 */



#include "main.h"
#include "Functions/library.h"



/**
 * @brief Checks if (i,j) is a canonical pair.
 *
 * @date 23-may-2013
 *
 * @param i Nucleotide position of the sequence, paired to j, where i < j
 * @param j Nucleotide position of the sequence, paired to i, where i < j
 *
 * @todo define CLEARLY what Canonical pairing is -- THIS includes Wobbly pairing - KTurnMotif does NOT!!!!!!!
 * @todo ?? Add argument "Wobbly?"
 * @todo Put this function in a separate file and remove it from Zuker class?
 *
 * @return wether i and j can for a canonical pairing
*/
bool isCanonicalPairing(char i, char j, bool arg_allowWobbly = true)
{
	if(enumeratePairing(i, j) != PAIRING_NONE)
	{
		return true;
	}
	else
	{
		return false;
	}
}
